WormBase-Caltech Weekly Calls
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Contents
Previous Years
2014 Meetings
April 3, 2014
WOBr
- Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser)
- As one-offs, Raymond can take newly generated GAFs from curators and process for testing.
Murray Expression datasets
- Still need to acquire primary expression data from Waterston lab
- Problems with handling inferred expression of genes in cells
- Thus inferred expression data will be removed
- Expression object will retain graphical representations supplied by Murray et al.
- A friendly reminder will be sent to Waterston requesting tabulated, processed primary expression data.
April 10, 2014
Apologies
- Karen: attending impromptu OICR group meeting, won't be on the Caltech call.
BioCurator Meeting
- many text mining tools
- many ontology systems, mapping ontologies
- Aging ontologies
- Anatomy ontology mapping (Uberon)
- Format convergence? OBO, OWL, RDF? Plugin for Protege to read OBO files
- How extensive is OWL? How much has OWL been applied to biology? OWL is being used for reasoning
- Community Annotation
- CANTO (Community ANotation TOol) workshop (Wen attended)
- PombeBase use CANTO and works well
- CANTO (Community ANotation TOol) workshop (Wen attended)
- Big data curation open discussion/workshop
- Enormous datasets (e.g. genome sequencing of all cancer patients)
- Data storage issue
- Data stability issue
- Clinical data, portal set up by Michael Cherry, ClinGen
- Lincoln's talk
- International Cancer Genome Consortium (ICGC) project (petabyte datasets)
- 10,000 cancer patients already sequenced (18 PB by 2018)
- Torent P2P data sharing
- BioCreative workshop
- Text mining
- Pubtator (http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/index.cgi?user=User425569566)
- Curates sentences, marks up entities, only applied to abstract
- Pubtator (http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/index.cgi?user=User425569566)
- GO annotation
- GO Cat (http://eagl.unige.ch/GOCat/)
- Text mining
- Amazon "Mechanical Turk" community annotation
- EcoCyc, MetaCyc - pathway curation (will hear from Karen)
- Reactome
- May be a good tool for displaying TF-target gene interaction display (vs. Cytoscape)
- Add a Reactome display to WormBase?
- SPELL - anything to replace SPELL? No.
- Still lacking other tools for microarray and RNA-Seq data
Heartbleed SSL security issue
- Raymond updated all servers/machines
- All machines need to be rebooted
- Any user passwords should be changed
- Do we care about any non-root users? Best to change all passwords on machines that have been updated
BioGrid C. elegans physical interactions
- Kimberly has been using BioGrid's curation tool
- We have a table of C.elegans large scale genetic and physical interaction data
- We're still trying to get all data
Timestamps
- Curator evidence vs. history of curation
- Kevin and Juancarlos still looking for use-cases
- Need to consider for future database migration and potential use of a common central database
- Curators use timestamps for culling out bogus data objects/cleaning up data
April 17, 2014
BioGrid followup
What are the roadblocks to protein-protein interaction curation and incorporation into WormBase?
AmiGO verification manager
Poster by PomBase Val Wood on GO annotation rules built through a co-annotation analysis.
I'm thinking this would be a good tool for analyzing and setting rules for phenotype annotation.
http://amigo2.berkeleybop.org/cgi-bin/amigo2/matrix https://sourceforge.net/apps/trac/pombase/wiki/MatrixProject http://build.berkeleybop.org/job/check-shared-annotations/lastBuild/console
They can include worm checks in this project as well. I don't know what we would need to do for that.
I can send along Val's poster to anyone who wants to know more